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Pitfalls in the analysis of ancient human mtDNA

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chinese Science Bulletin 2003年第8期48卷 826-830页

作者： YAO Yonggang1,3.& zhang yaping1,2 1. laboratory of {3. Evolution and Genome Diversity, kunming institute of zoology, chinese academy of sciences, kunming 650223. china 2. laboratory for Conservation and Utilization of Bio-resource, Yunnan University, kunming 650091, china 3. Graduate School of the chinese academy of sciences, Beijing 10003., china Correspondence should be addressed to zhang {13. (e-mail: zhang- yp1@***) laboratory of molecular Evolution and Genome Diversity Kunming Institute of Zoology Chinese Academy of Sciences Kunming 650223 China Graduate School of the chinese academy of sciences Beijing 100039 China laboratory for Conservation and Utilization of Bio-resource Yunnan University Kunming 650091 China

The retrieval of DNA from ancient human specimens is not always successful owing to DNA deteriora-tion and contamination although it is vital to provide new insights into the genetic structure of ancient people and to reconstruct the past history. Normally, only short DNA fragments can be retrieved from the ancient specimens. How to identify the authenticity of DNA obtained and to uncover the information it contained are difficult. We employed the ancient mtDNAs reported from Central Asia (including Xin-jiang, china) as an example to discern potentially extraneous DNA contamination based on the updated mtDNA phylog-eny derived from mtDNA control region, coding region, as well as complete sequence information. Our results demon-strated that many mtDNAs reported are more or less prob-lematic. Starting from a reliable mtDNA phylogeney and combining the available modern data into analysis, one can ascertain the authenticity of the ancient DNA, distinguish the potential errors in a data set, and efficiently decipher the meager information it harbored. The reappraisal of the mtDNAs with the age of more than 2000 years from Central Asia gave support to the suggestion of extensively (pre)historical gene admixture in this region.

关键词：古代人类遗传构造 DNA 脱氧核糖核酸

Melanocortin-1 receptor gene variants in four chinese ethnic populations

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Cell Research 2001年第1期11卷 81-84页

作者： SHI PENG, XUE MEI LU, HUAI RONG LUO, JIN-GONG XIANG-YU, YA PING zhang (laboratory of cellular and {3. Evolution, kunming institute of zoology, the chinese academy of sciences, kunming 650223. china) laboratory of cellular and molecular Evolution Kunming Institute of Zoology the Chinese Academy of Sciences Kunming China

There is strong relationship between melanocortin-1 receptor (MCIR) gene variants and human hair color and skin type. Based on a sequencing study of MC1R gene in 50 individuals from the Uygur, Tibetan, Wa and Dai ethnic populations, we discuss the occurrence of 7 mc1r variants consisting of 5 nonsynonymous sites (Val60Leu, Arg67Gln, Val92Met, Arg163.ln and Ala299Val) and 2 synonymous sites (C414T and A942G), among which C414T and Ala299Val were reported for the first time. Confirmation and analysis were the made of 122 individuals at three common point mutations (Val92Met, Arg163.ln, A942G) using PCR-SSCP. The frequency of Arg163.ln variant varies in the four ethnic populations, with percentage of 40%, 85.0%, 66. 2% and 72.7%, respectively, while those of Val92Met and A942G are roughly similar in these four populations. The different environments, migration and admixture of various ethnic groups in china might have impact on the observed frequency of Arg163.ln.

关键词： MC1R gene ethnic populations nonsynonymous site synonymous site.

molecular evolution of stress-response gene Leptin in high-altitude chinese snub-nosed monkeys (Rhinopithecus genus)

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chinese Science Bulletin 2010年第36期55卷 4132-4135页

作者： WANG XiaoPing1,2, JIN Wei1,2, YU Li1,2 & zhang yaping1,2 1 laboratory for Conservation and Utilization of Bio-resource, Yunnan University, kunming 650091, {3. 2 State Key laboratory of Genetic Resources and Evolution, kunming institute of zoology, chinese academy of sciences, kunming 650223. china laboratory for Conservation and Utilization of Bio-resource Yunnan University Kunming China State Key laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming China

chinese snub-nosed monkeys (genus Rhinopithecus, subfamily Colobinae), including R. bieti, R. brelichi and R. roxellana, are well-known as the non-human primates with the highest known altitudinal distribution. They represent an interesting model organism of adaptation to the extreme environmental stresses. However, no study at the molecular level has yet been reported for the high-altitude adaptation in chinese snub-nosed monkeys. Leptin, as an adipocyte-derived hormone, is believed to play an important role in energy homeostasis in adaptation to high altitude environments. In the present study, we sequenced and compared leptin sequences of the chinese snub-nosed monkeys (R. bieti and R. roxellana) with their lowland close relative R. avunculus and other Colobines. Unexpectedly, no amino acid changes were observed in the 7 Colobinae species examined, including the 2 chinese snub-nosed monkeys, indicating no difference in the evolutionary pattern of the Leptin gene between high-altitude monkeys and their lowland counterparts. In contrast to a previous finding of adaptive evolution of Leptin gene in plateau pikas, our study suggests that this gene may not have an important role in high-altitude adaptation of chinese snub-nosed monkeys. Other nuclear genes associated with energy metabolism, or mitochondrial genes, are most likely to be involved the molecular mechanism underlying adaptation of these monkeys to cold and hypoxia associated with the highland environment.

关键词： Leptin基因金丝猴属瘦素基因压力反应分子进化高空鼻极端环境

Evolution of cd59 gene in mammals

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Science china(Life sciences) 2007年第6期50卷 773-779页

作者： GONG YuanYing1,2, PENG MinSheng1,2, ZHOU WeiPing1,3.4 & zhang yaping1,4 1 State Key laboratory of Genetic Resources and Evolution,{3., chinese academy of sciences, kunming 650223. china 2 Graduate University of the chinese academy of sciences, Beijing 100049, china 3.molecular and Cell Biology, University of Science and Technology of china, Hefei 23.026, china 4 laboratory for Conservation and Utilization of Bio-resources, Yunnan University, kunming 650091, china State Key laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming China Graduate University of the chinese academy of sciences Beijing China molecular and Cell Biology University of Science and Technology of China Hefei China laboratory for Conservation and Utilization of Bio-resources Yunnan University Kunming China

The CD59-coding sequences were obtained from 5 mammals by PCR and BLAST, and combined with the available sequences in GenBank, the nucleotide substitution rates of mammalian cd59 were calcu- lated. Results of synonymous and nonsynonymous substitution rates revealed that cd59 experienced negative selection in mammals overall. Four sites experiencing positive selection were found by using "site-specific" model in PAML software. These sites were distributed on the molecular surface, of which 2 sites located in the key functional domain. Furthermore, "branch-site-specific" model detected 1 positive site in cd59a and cd59b lineages which underwent accelerated evolution caused by positive selection after gene duplication in mouse.

关键词： cd59, evolution, positive selection

Evolutionary implications of Avian Infectious Bronchitis Virus(AIBV)analysis

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Cell Research 2006年第3期16卷 323-327页

作者： Peng Shi~(1,2) Li Yu~2 Yun-xin Fu~3.Jing-Fei Huang~1 Ke-Qin zhang~2 Ya-ping zhang~(1,2)1 laboratory of {3. and molecular Evolution,and molecular Biology of Domestic Animals,kunming lnstitute of zoology,chinese academy of sciences,kunming 650223.{13. 2 laboratory for Conservation and Utilization of Bio-resource,Yunnan University,kunming 650091,{13. 3.Human Genetics Center,University of Texas at Houston,Houston,Texas 7703.,USA laboratory of cellular and molecular Evolution and Molecular Biology of Domestic Animals Kunming Institute of Zoology Chinese Academy of Sciences Kunming 650223 China.

For developing efficient vaccines,it is essential to identify which amino acid changes are most important to the sur-vival of the *** investigate the amino acid substitution features in the Avian Infectious Bronchitis Virus (AIBV)antigenic domain of a vaccine serotype (DE072) and a virulent viral strain (GA98) to better understand adaptive evo-lution of *** addition,the SARS Coronavirus (SARS-CoV) was also analyzed in the same *** is interestingto find that extreme comparability exists between AIBV and SARS in amino acid substitution *** suggests thatamino acid changes that result in overall shift of residue charge and polarity should be paid special attention to duringthe development of vaccines.

关键词： Avian Infectious Bronchitis Virus SARS Coronavirus positive selection adaptive evolution vaccine development

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不具有3.碱基周期性的编码序列初探

生物化学与生物物理进展 2002年第2期29卷 267-272页

作者：张静石秀凡云南大学应用统计中心昆明650091 中国科学院昆明动物研究所昆明650223

对 12 0个较短编码序列 (<12 0 0bp)的Fourier频谱进行分析表明 ,3.碱基周期性在短编码序列中并不是绝对存在的 .统计分析提示 ,编码序列有无 3.碱基周期性与序列的碱基组成和分布、所编码蛋白质氨基酸的选用和顺序以及同义密码子的使... 详细信息

对 12 0个较短编码序列 (12 0 0bp)的Fourier频谱进行分析表明 ,3.碱基周期性在短编码序列中并不是绝对存在的 .统计分析提示 ,编码序列有无 3.碱基周期性与序列的碱基组成和分布、所编码蛋白质氨基酸的选用和顺序以及同义密码子的使用都有一定的关系 .一般地 ,非周期 3.列中A +U含量高于G +C含量 ,周期 3.列的情况则相反 ;非周期 3.列中碱基在密码子三个位点上的分布比周期 3.列中的分布均匀 ;非周期 3.列密码子和氨基酸的使用偏向没有周期 3.列的大 .在利用Fourier分析方法预测DNA序列中的基因和外显子时。

关键词：编码序列 Fourier分析 3.碱基周期性非3.碱基周期性

Rhizosphere microbial markers (micro-markers): A new physical examination indicator for traditional chinese medicines

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chinese Herbal Medicines 2024年第2期16卷 180-189页

作者： Kailin yang yaping Zheng Kangmeng Sun Xinyan Wu Zheng zhang Chunnian He Peigen Xiao institute of Medicinal Plant Development Chinese Academy of Medical Sciences&Peking Union Medical CollegeBeijing 100193China Key laboratory of Bioactive Substances and Resources Utilization of chinese Herbal Medicine Ministry of EducationBeijing 100193China

Rhizosphere microorganisms,as one of the most important components of the soil microbiota and plant holobiont,play a key role in the medicinal plant-soil ecosystem,which are closely related to the growth,adaptability,nutrient absorption,stress tolerance and pathogen resistance of host *** recent years,with the wide application of molecular biology and omics technologies,the outcomes of rhizosphere microorganisms on the health,biomass production and secondary metabolite biosynthesis of medicinal plants have received extensive ***,whether or to what extent rhizosphere microorganisms can contribute to the construction of the quality evaluation system of chinese medicinal materials is still *** on the significant role of rhizosphere microbes in the survival and quality formation of medicinal plants,this paper proposed a new concept of rhizosphere microbial markers(micro-markers),expounded the relevant research methods and ideas of applying the new concept,highlighted the importance of micro-markers in the quality evaluation and control system of traditional chinese medicines(TCMs),and introduced the potential value in soil environmental assessment,plant pest control and quality assessment of *** provides reference for developing ecological planting of TCMs and ensuring the production of high quality TCMs by regulating rhizosphere microbial communities.

关键词： physical examination indicator quality evaluation quality formation of medicinal plants rhizosphere microorganisms rhizosphere microbial markers

Nerve Growth Factor Prevents the Apoptosis-associated Increase in Acetylcholinesterase Activity after Hydrogen Peroxide Treatment by Activating Akt

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Acta Biochimica et Biophysica Sinica 2007年第1期39卷 46-56页

作者： Hua JIANG~(1,3. Jingya zhang~(1,3. hui ZHU~(1,3. Hong LI~2 and Xuejun zhang~1 ~1{3. of molecular Cell Biology,institute of Biochemistry and Cell Biology,Shangha institutes for Biological sciences,chinese academy of sciences,Shanghai 20003.,china ~2DEFEMA,Faculté de Medecine et de Pharmacie,University of Rouen,Rouen 76821,France ~3.raduate school of the chinese academy of sciences,Beijing 100080,china laboratory of molecular Cell Biology Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of SciencesShanghai 200031 China Graduate school of the chinese academy of sciences Beijing 100080 China DEFEMA Faculté de Medecine et de Pharmacie University of RouenRouen 76821 France

Acetylcholinesterase （ACHE） is thought to play an important role during *** resultsshowed that H2O2induced AChE activity,a functional marker in apoptosis,increases in neuronal-like PC ***, which is involved in cellular redox homeostasis,inhibited the increase of AChE activity,suggesting that reactive oxygen species （ROS） play a key role in this *** investigation showedthat the elevation of AChE was observed after the degradation of Akt, release of cytochrome c from mitochondriainto the cytosol,and activation of caspase family *** nerve growth factor （NGF） was present,with the maintenance of Akt level,the elevation of AChE,the cytochrome c diffusion,as well as apoptosiswere markedly attenuated in H202-treated PC 12 cells. However,wortmannin,an inhibitor of the PI3./Aktpathway,accelerated the apoptosis and increased the AChE *** overexpression of constitutivelyactivated Akt,which is a downstream signalling element of the NGF receptor TrkA,delayed mitochondrialcollapse and inhibited elevation of AChE ***, NGF prevented apoptosis and elevation of AChEactivity by activating the Akt pathway and stabilizing the function of mitochondria.

关键词： acetylcholinesterase(AChE) reactive oxygen species(ROS) Akt apoptosis

酵母内含子在基因序列中的分布对基因转录效率的影响

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生物化学与生物物理进展 2003年第6期30卷 945-949页

作者：张静石秀凡杨恒芬云南大学应用统计中心中国科学院昆明动物研究所

对酵母中高效转录和低效转录基因内含子序列寡核苷酸使用情况的对照分析 ,显示两类内含子的序列结构有差异 ,并且高效转录基因内含子序列含有较多潜在的转录因子结合位点 ,由此推测内含子可能参与基因转录的调控 .这个结论有待更多的数... 详细信息

对酵母中高效转录和低效转录基因内含子序列寡核苷酸使用情况的对照分析 ,显示两类内含子的序列结构有差异 ,并且高效转录基因内含子序列含有较多潜在的转录因子结合位点 ,由此推测内含子可能参与基因转录的调控 .这个结论有待更多的数据证实 .对内含子和外显子在两组基因序列中的分布 (长度、位置等 )进行详细比较分析后显示 ,高效转录基因内含子和低效转录基因内含子的长度有比较明显的界限 .两组基因中外显子长度的均值虽然有些差异 ,却没有明显的界限 .基因序列长度与外显子长度的情况相似 .虽然内含子的相对位置在两类基因中都很靠近 5′端 ,但是从实际位置看 ,高效转录基因中比较多的内含子很靠近基因的 5′端 ,有些则位于 5′ UTR区域 .这些结果提示 ,基因的转录效率与内含子的长度有关 ,与外显子及基因序列的长度无关 ,内含子的位置也可能影响转录效率 ,内含子对基因转录的调控可能与基因上游的转录调控有关联。

关键词：酵母基因转录频率内含子长度内含子位置基因序列基因转录